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Chemistry software included

Software Description Links
Ghemical An interactive program for molecular mechanics and quantum-mechanical calculations. Friendly GUI. More Home page
Jmol Molecular viewer. More User Guide
MPQC The Massively Parallel Quantum Chemistry Program. More Manual
Open Babel Converts between different file formats for computational chemistry applications More Formats
PSI3 Ab-initio quantum chemistry package. More User manual
Rasmol Molecular visualization program More Home page
XDrawChem 2-D molecule drawing program More Manual


Version: 1.01 License: GPL
Description: Ghemical a very versatile simulation engine for molecular modeling and quantum-mechanical calculations. Its friendly GUI is suitable for beginners.


Version: 9 License: GPL
Description: Jmol is a free, open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.

User Guide


Version: 2.2.2 License: GPL
Description: MPQC computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. It runs on a wide range of architectures ranging from individual workstations to symmetric multiprocessors to massively parallel computers. Its design is object oriented, using the C++ programming language.
  • Closed shell, unrestricted and general restricted open shell Hartree-Fock energies and gradients
  • Closed shell, unrestricted and general restricted open shell density functional theory energies and gradients
  • Second order open shell perturbation theory (OPT2[2]) and Z-averaged perturbation theory (ZAPT2) energies.
  • Second order closed shell Møller-Plesset perturbation theory energies and gradients.
  • Second order Møller-Plesset perturbation theory including an R12 correlation factor using an auxilary basis set [(ABS) MP2-R12]. Energies of closed-shell systems are supported.
  • Robust internal coordinate geometry optimizer that efficiently optimizes molecules with many degrees of freedom. Nearly arbitrary internal coordinate constraints can be handled.
Introductory talk

Open Babel

Version: 1.100.2 License: GPL
Description: Open Babel is a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.
List of supported file formats


Version: 3.2.2 License: GPL
Description: The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package's current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and multi-reference configuration interaction models. Molecular point-group symmetry is utilized throughout to maximize efficiency. The latest version of the code, PSI 3.2, rests upon a completely rewritten infrastructure relative to previous versions of the package. Non-standard computations are possible using a customizable input format. Package highlights include:
  • Arbitrarily high angular momentum levels in integrals and derivative integrals. (Up to k-type functions have been tested.)
  • Coupled cluster methods including CCSD and CCSD(T) with RHF, ROHF, UHF, and Brueckner orbitals.
  • Determinant-based CI including CASSCF, RAS-CI, and Full CI.
  • Multithreaded integral-direct SCF, MP2, and MP2-R12.
  • Excited state methods: CIS, CIS(D), RPA, and EOM-CCSD.
  • Analytic energy gradients for CCSD with RHF, ROHF, and UHF orbitals.
  • Coupled cluster linear response methods for static and dynamic polarizabilities and optical rotation.
  • Diagonal Born-Oppenheimer correction (DBOC) for RHF, ROHF, UHF, and CI wave functions.
User manual


Version: License: click here
Description: RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The program has been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structure Department at Glaxo Research and Development, Greenford, UK.

RasMol reads in molecular co-ordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations.

Currently supported input file formats include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XMol XYZ format and CHARMm format files. If connectivity information and/or secondary structure information is not contained in the file this is calculated automatically.


Version: 1.8.5 License: GPL
Description: XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.

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Content owner: Pratul K. Agarwal,
Updated: Thursday, 14-Dec-06 14:33:14 PST